[{values:[{"id":"123","val":true},{"id":"456","val":true},{"id":"789","val":false},]},{values:[{"id":"123","val":true},{"id":"123","val":true},{"id":"123","val":false},]},{values:[{"id":"234","val":false},{"id":"567","val":false}]}]

db.collection.find({values:{"$elemMatch":{val:true}},$expr:{$gte:[{$reduce:{input:"$values",initialValue:0,in:{$sum:["$$value",{$cond:[{$eq:["$$this.val",true]},1,0]}]}}},2]}})